[Freesurfer] recon-all cuda version 9.2 and 8.0

External Email - Use Caution Hi all How to download recon-all with GPU9.2 or 8.0? Thanks. Best 2018-07-24 charujing123 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesur

[Freesurfer] ICV as covariate for controls vs. patients

External Email - Use Caution Hello experts, I am interested in identifying regions of interest by comparing cortical volume (CV) between controls and patients. After including age and sex as my covariates, I identified regions X1 and X2, which showed significantly lower CV for pa

Re: [Freesurfer] mris_ca_label seed

Hi Rosemary, the seeds for those commands are set from recon-all. The individual binaries do not seed themselves with a default value, so it’s expected that mris_ca_label produces inconsistent results when run independently (and without the -seed flag). The algorithm processes the surface verti

Re: [Freesurfer] Selecting vertices on label boundary for analysis

Hi Jacob I don't think we have a binary to do this, but it should be easy enough in matlab (just look for vertices that are in the label and have neighbors that are not) cheers Bruce On Mon, 23 Jul 2018, Jacob Miller wrote: External Email - Use Caution Hi Freesurfer team,

[Freesurfer] Selecting vertices on label boundary for analysis

External Email - Use Caution Hi Freesurfer team, In tksurfer, it's possible to display the outline of a label. Is there is a way to obtain the list of vertices that make up the outline of a label, so that I may select them from the label file? My goal is to perform an analysis th

[Freesurfer] mris_ca_label seed

External Email - Use Caution Hello, I am running a dataset through version 6.0 of Freesurfer on Linux, extracting results for both the Desikan atlas and our own atlas. When extracting the stats for our atlas, the results were varying considerably (sometimes up to 10%) in test-re

[Freesurfer] symbolic link problem

External Email - Use Caution Hi, Running recon-all on sag T1 post-contrast MRI (for archival study) on virtualBox with centOS7 and freesurfer 6. The virtual box runs on a windows server and is allocated 8 processors and 16 GB memory by the windows server on which it resides. A

[Freesurfer] Fwd: The results of your email commands

External Email - Use Caution Dear experts, We are looking for a correlation between functional and structal ROIs on FSL and Freesurfer, but we have some questions about the atlas. 1. Are the Juelich Histological Atlas that can be downloaded with FSL the same as the cortical parc

Re: [Freesurfer] adding additional manually-defined labels to atlas-derived .annot file

Your workflow looks right. Once you have a set of labels you want to combine, use mris_label2annot. You will have to supply a color tab (--ctab) that you have modified to include the new label. To mediate between multiple labels having the same vertex, use the --maxstatwinner option. You will h

Re: [Freesurfer]

Hi Ziqian it really depends on the specifics of the tumor. If it is interior to the white matter and you have a mask you could try pasting that into the wm.mgz as "edited" wm (that is, set those wm.mgz voxels to 255) cheers Bruce On Mon, 23 Jul 2018, 王子谦 wrote: External Email -

Re: [Freesurfer] adding additional manually-defined labels to atlas-derived .annot file

Hi James yes, I guess that is the right workflow. YOu will also need to modify the color lut to include your new parcel. As for overlap you could just remove it in matlab I guess. Or maybe mris_label2annot handles it, I'm not sure (Doug may know) cheers Bruce On Mon, 23 Jul 2018, James Hobar

Re: [Freesurfer] Hippocampal and amygdala subfields

Hi Zheng I guess you could edit it with freeview if you had to. cheers Bruce On Mon, 23 Jul 2018, 郑凤莲 wrote: External Email - Use Caution Hi experts, I am using FS dev version for hippocampal and amygdala subfields. It's an  automatic progress. Reviewers suggested that "Wa

Re: [Freesurfer] (no subject)

Hi Maedeh in your command line you need a space between the 'n' and the '2', so it should be: -n 2 not -n2 cheers Bruce On Mon, 23 Jul 2018, Maedeh Khalilian wrote: External Email - Use Caution Dear FreeSurfer experts, I would like to use the FreeSurfer package to do a

[Freesurfer] nu_estimate_np_and_em and nu_correct error during recon-all

External Email - Use Caution Hello FreeSurfer Developers, I'm attempting to create a head model with T1w by creating tetrahedral head mesh with the simnibs program (documentation_2.0.1_preprocessing_scripts.pdf

[Freesurfer] PhD Studentship available at UCL

External Email - Use Caution **Apologies for the wide distribution** Dear All, We have a PhD studentship for developing neuroimaging outcome measures in progressive multiple sclerosis clinical trials. The student will work with Prof Ciccarelli, Dr Chard and myself. https://www.f

[Freesurfer]

External Email - Use Caution Hi, I am trying to do connectome to my patient with glioma. But now I’m stuck in parcellation the T1 image. Because the chaotic intensities of tumor totally mess up the outcome. Do you guys have any suggestion to the tumor? Is it any command about m

[Freesurfer] Re?? segmentHA_T2.sh

External Email - Use Caution Thanks, I am very sorry for the late reply. I didn't have a machine with more RAM at present,but i ran the code on another machine(mac mini,4G or 8G LPDDR3 SDRAM ,500GB) several month ago. it ran well.so i didn't certain it. I will try to test the

Re: [Freesurfer] adding additional manually-defined labels to atlas-derived .annot file

External Email - Use Caution Good Morning All, Just wondering if anyone had any advice regarding this problem? I am still struggling to get things running as intended! Any help would be greatly appreciated. BW James On Tue, Jun 26, 2018 at 1:20 PM, James Hobart wrote: > Hi F

[Freesurfer] Hippocampal and amygdala subfields

External Email - Use Caution Hi experts, I am using FS dev version for hippocampal and amygdala subfields. It's an automatic progress. Reviewers suggested that "Was the hippocampal and amygdala segmentation visually inspected?" We have visually inspected the segmentation and the